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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #294643

Title: Diversity and heritability of the maize rhizosphere microbiome under field conditions

item PEIFFER, JASON - Cornell University
item SPOR, AYME - Cornell University
item KOREN, OMRY - Cornell University
item JIN, ZHAO - Cornell University
item TRINGE, SUSANNAH GREEN - Department Of Energy Joint Genome
item DANGL, JEFFERY - University Of North Carolina
item Buckler, Edward - Ed
item LEY, RUTH - Cornell University

Submitted to: Proceedings of the National Academy of Sciences (PNAS)
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/15/2013
Publication Date: 4/16/2013
Citation: Peiffer, J.A., Spor, A., Koren, O., Jin, Z., Tringe, S., Dangl, J.L., Buckler IV, E.S., Ley, R.E. 2013. Diversity and heritability of the maize rhizosphere microbiome under field conditions. Proceedings of the National Academy of Sciences. 110(16):6548-6553.

Interpretive Summary: The maize rhizosphere, or interface between roots and soil, is adapted to regulate the exchange of resources and promote plant growth. Maize exudes substantial proportions of the carbon it fixes through its roots as organic acids, sugars, and aromatics. Many of these exudates influence local soils and help to recruit or deter colonization of bacterial communities. Given the exceptional genetic diversity of maize, and its ability to adapt to local environments, we inferred there may be a heritable component to the ability of maize to affect these microbiota. To test this hypothesis, we planted 27 diverse maize inbreds in five field environments. At flowering time, roots were extracted from the soil. From each sample, the 16s rRNA gene was sequenced from total DNA. After aligning sequence data to known bacterial DNA, the relative abundances of bacterial taxa were inferred. Substantial variation in microbial diversity was observed between fields, and between the rhizosphere and soil. A small but significant proportion of variation in microbial diversity was also found between inbreds, with a larger proportion of variation in microbial diversity identified between inbreds within a field. These results suggest the ability of maize to affect its microbial communities is heritable. They lay a foundation for analysis of the genes and specific microbial species influenced by the plant and will ultimately lead to methods exploiting maize-microbe interactions during crop improvement.

Technical Abstract: The rhizosphere is a critical interface supporting the exchange of resources between plants and their associated soil environment. Rhizosphere microbial diversity is influenced by the physical and chemical properties of the rhizosphere, some of which are determined by the genetics of the host plant. However, within a plant species, the impact of genetic variation on the composition of the microbiota is poorly understood. Here, we characterized the rhizosphere bacterial diversity of 27 modern maize inbreds possessing exceptional genetic diversity grown under field conditions. Randomized and replicated plots of the inbreds were planted in five field environments in three states, each with unique soils and management conditions. Using pyrosequencing of bacterial 16S rRNA genes, we observed substantial variation in bacterial richness, diversity, and relative abundances of taxa between bulk soil and the maize rhizosphere, as well as between fields. The rhizospheres from maize inbreds exhibited both a small but significant proportion of heritable variation in total bacterial diversity across fields, and substantially more heritable variation between replicates of the inbreds within each field. The results of this study should facilitate expanded studies to identify robust heritable plant–microbe interactions at the level of individual polymorphisms by genome wide association, so that plant-microbiome interactions can ultimately be incorporated into plant breeding.